Place a 5-quart Dutch oven over medium heat. Add the oil and butter to the pan and heat until the butter is melted.
Reduce the heat to low and add the sliced onions and 1 teaspoon salt to the hot pan. Cook, stirring often with a wooden spoon, until the onions are deep golden brown, about 1 hour and 45 minutes.
To the onions add the garlic, sage and thyme to the pan and stir to combine. Continue to cook, stirring occasionally to prevent sticking, until the garlic is fragrant, about 2 minutes.
Deglaze the pan with the beer and the sherry. Stir to combine, scraping the bottom of the pan to release any brown bits that may have formed. Simmer over medium low heat until the liquid is fully reduced, about 2 minutes.
Add broth and remaining 1 1/4 teaspoon salt. Bring to a boil over medium high heat. Reduce heat to low and allow the soup to simmer for 20 to 30 minutes. Season with the black pepper and finish with the lemon juice.
Preheat the oven 375 degrees F.
Meanwhile, heat a large ovenproof skillet over medium heat. Melt the stock dripping in the pan and add the baguette. Flip the slices to cully coat in the fat. Season with the salt. Place the pan in the oven and bake until golden and crispy, about 10 minutes.
When ready to serve, heat a griddle over medium low heat.
Ladle the soup evenly among 4 bowls leaving about 1 inch of space at the top of each bowl.
Brush the griddle lightly with olive oil. Sprinkle 1/3 cup of cheese in 8 different spots on the griddle and top the cheese with a crouton. When the cheese is melted and browned in spots, use an offset spatula to scoop up the cheesy crouton on a flip on top of the soup placing 2 croutons on each serving.
Sprinkle with thyme leaves and/or Jalapeno Seasoning if using and serve immediately.